gmx_qk
Good day and welcome to the gmx_qk!!. This is a Zenity, Python and gromacs dependent bash program. It is designed for beginners to the gromacs who would like to simulate the Protein-Ligand Complex. Gmx_qk is a fully automated program that works well with Gromacs versions 5.0 and 2021.4.
Informative and question widgets are supported by Zenity (GUI).
https://github.com/harry-maan.
About

Workflow

Installation gmx_qk
- Download the package from
- Open the terminal and run “bash configure.sh” gmx_qk will be appeared in the applications menu.
- Click on gmx_qk

Step 1: Launching gmx_qk in terminal
- Open the terminal and run “gmx_qk”

Step 2: Select gromacs
- Select executable gromacs usually gromacs installed in /usr/local/ or /opt

Step 2: Select Protein or Receptor file
- This is a zenity supported widget “Please select a receptor file (.pdb)
- Receptor file can be downloaded from https://www.rcsb.org/
- Make your receptor file clean using https://charmm-gui.org/ or whatever else you are familiar to the protein preparation tools.
- Remove all the hetero atoms i.e., ions, ligand, free water or solvent.

Step 3: Select a ligand file (.pdb)
- This is a zenity supported widget “Please select a ligand file (.pdb)
- ligand file can be downloaded from https://pubchem.ncbi.nlm.nih.gov/ as 3D .sdf or copy Canonical SMILES and paste in the http://zarbi.chem.yale.edu/ligpargen/
- Download the zipped file from ligpargen sever.
- Extract zip file which has name.pdb and name.itp(required for next step)

Step 4: Select a ligand parameter file (.itp)
- This is a zenity supported widget “Please select a ligand file (.itp)
- .itp file generated via http://zarbi.chem.yale.edu/ligpargen/ in the zipped file.(Downloaded in the last step)

Step 6: Output file and its content
